I'm trying to get my Zaurus SL6000 to be able to communicate in a very basic way with a micro controller I have (with a ZThinCable). I'd like to move up to writing my own apps that can use it later... but thats a different story.

So, anyways, the microcontroler is set to put out a continious stream of 123123123123123. This shows up fine in serial-monitors for windows. The problem I've run into: I can figure out how to de-assert DTR in linux. DTR resets the microcontroler, so having DTR asserted hangs it in a loop. I know I have the right port however. I made it so a light on the microcontroller is on when running, and off while being reset. The moment I the light turns off and the console just hangs there. No input because the device is constantly resetting. However, if I open a second terminal and the light comes back on. I've done some googling, and most sites say that I need to set but, the stty on my Z doesnt recognize that as a valid argument. Help?

I'd suggest looking at the kernel serial_pxa200 driver and cutting it directly there. It can also work as a module.